mergeData: Merge curatedMetagenomicData List

In waldronlab/curatedMetagenomicData: Curated Metagenomic Data of the Human Microbiome

Merge curatedMetagenomicData List

Description

To merge the list elements returned from curatedMetagenomicData into a single SummarizedExperiment or TreeSummarizedExperiment object, users will use mergeData() provided elements are the same dataType (see returnSamples). This is useful for analysis across entire studies (e.g. meta-analysis); however, when doing analysis across individual samples (e.g. mega-analysis) returnSamples is preferable.

Usage

mergeData(mergeList)

Arguments

mergeList

a list returned from curatedMetagenomicData where all of the elements are of the same dataType (see returnSamples)

Details

Internally, mergeData() must full join assays and rowData slots of each SummarizedExperiment or TreeSummarizedExperiment object (colData is merged slightly more efficiently by row binding). While dplyr methods are used for maximum efficiency, users should be aware that memory requirements can be large when merging many list elements.

Value

when mergeList elements are of dataType (see returnSamples) relative_abundance, a TreeSummarizedExperiment object is returned; otherwise, a SummarizedExperiment object is returned

See Also

curatedMetagenomicData, returnSamples

Examples

curatedMetagenomicData("LiJ_20.+.marker_abundance", dryrun = FALSE) |>
    mergeData()

curatedMetagenomicData("LiJ_20.+.pathway_abundance", dryrun = FALSE) |>
    mergeData()

curatedMetagenomicData("LiJ_20.+.relative_abundance", dryrun = FALSE) |>
    mergeData()

waldronlab/curatedMetagenomicData documentation built on Nov. 4, 2024, 7:57 a.m.